Related papers: Guessing the upper bound free-energy difference be…
The energy distance and energy scores became important tools in multivariate statistics and multivariate probabilistic forecasting in recent years. They are both based on the expected distance of two independent samples. In this paper we…
A novel thermodynamic integration (TI) scheme is presented that allows computing the free energy of grain boundaries (GBs) in crystals from atomistic computer simulation. Unlike previous approaches, the method can be applied at arbitrary…
Protein denaturing induced by supercooling is interpreted as a process where some or all internal symmetries of the native protein are spontaneously broken. Hence, the free-energy potential corresponding to a folding-funnel landscape…
Only about 1,000 qualitatively different protein folds are believed to exist in nature. Here, we review theoretical studies which suggest that some folds are intrinsically more designable than others, {\it i.e.} are lowest energy states of…
Explicit expressions for quantum fluctuations of energy in subsystems of a hot relativistic gas of spin-$1/2$ particles are derived. The results depend on the form of the energy-momentum tensor used in the calculations, which is a feature…
We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wildtype structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of…
The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
The results of minimal model calculations suggest that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By mean of molecular dynamics simulations around the native…
We study continuity, and lack thereof, of thermodynamical properties for one-dimensional dynamical systems. Under quite general hypotheses, the free energy is shown to be almost upper-semicontinuous: some normalised component of a limit…
Assuming that mutation and fixation processes are reversible Markov processes, we prove that the equilibrium ensemble of sequences obeys a Boltzmann distribution with $\exp(4N_e m(1 - 1/(2N)))$, where $m$ is Malthusian fitness and $N_e$ and…
Here we propose that the upper bound marginal stability of proteins (7.4 kcal/mol) is a universal property that includes macro-molecular complexes and is not affected by molecular changes such as mutations and Post-Translational…
For classical discrete systems under constant composition, it has been considered that genuine thermodynamic variables such as free energy cannot be generally determined from information about a single or a few selected microscopic states.…
Structural, electronic and thermodynamic properties of native defects in GaS and GaSe monolayers are investigated by means of accurate ab-initio calculations. Based on their charge transition levels we assess the influence of the studied…
Free energy calculation is critical in predictive tasks such as protein folding, docking and design. However, rigorous calculation of free energy change is prohibitively expensive in these practical applications. The minimum potential…
We consider a homogeneous Bose gas in the Gross-Pitaevskii limit at temperatures that are comparable to the critical temperature for Bose-Einstein condensation in the ideal gas. Our main result is an upper bound for the grand canonical free…
Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…
Self-assembling novel ordered structures with nanoparticles has recently received much attention. Here we use computer simulations to study a two-dimensional model system characterized by a simple isotropic interaction that could be…
Properties of the free energy landscape in phase space of a dense hard sphere system characterized by a discretized free energy functional of the Ramakrishnan-Yussouff form are investigated numerically. A considerable number of glassy local…
We investigate how a thermal boundary, modelled by a Langevin dynamics, affect the macroscopic evolution of the energy at different space-time scales.